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Nuclear body protein SP140 (Lymphoid-restricted homolog of Sp100) (LYSp100) (Nuclear autoantigen Sp-140) (Speckled 140 kDa)

 SP140_HUMAN             Reviewed;         867 AA.
Q13342; E7ESH9; E7EUR5; E9PFJ6; Q0VGE5; Q13341; Q3KR17; Q4ZG66;
Q53TG1; Q6NSG4; Q92881; Q96TG3;
15-JUL-1999, integrated into UniProtKB/Swiss-Prot.
16-DEC-2008, sequence version 2.
25-OCT-2017, entry version 160.
RecName: Full=Nuclear body protein SP140 {ECO:0000312|HGNC:HGNC:17133};
AltName: Full=Lymphoid-restricted homolog of Sp100 {ECO:0000303|PubMed:8695863};
Short=LYSp100 {ECO:0000303|PubMed:8695863};
AltName: Full=Nuclear autoantigen Sp-140 {ECO:0000303|PubMed:8910577};
AltName: Full=Speckled 140 kDa {ECO:0000303|PubMed:8910577};
Name=SP140 {ECO:0000312|HGNC:HGNC:17133};
Synonyms=LYSP100 {ECO:0000303|PubMed:8695863};
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS LYSP100-A AND LYSP100-B),
SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
PubMed=8695863;
Dent A.L., Yewdell J., Puvion-Dutilleul F., Koken M.H.M., de The H.,
Staudt L.M.;
"LYSP100-associated nuclear domains (LANDs): description of a new
class of subnuclear structures and their relationship to PML nuclear
bodies.";
Blood 88:1423-1426(1996).
[2]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM SP140), VARIANT LYS-516, FUNCTION,
SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND INDUCTION BY INTERFERON.
TISSUE=Placenta;
PubMed=8910577; DOI=10.1074/jbc.271.46.29198;
Bloch D.B., de la Monte S.M., Guigaouri P., Filippov A., Bloch K.D.;
"Identification and characterization of a leukocyte-specific component
of the nuclear body.";
J. Biol. Chem. 271:29198-29204(1996).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=15815621; DOI=10.1038/nature03466;
Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H.,
Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M.,
Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E.,
Kremitzki C., Oddy L., Du H., Sun H., Bradshaw-Cordum H., Ali J.,
Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C.,
Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J.,
Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A.,
Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K.,
Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M.,
Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K.,
McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C.,
Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N.,
Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M.,
Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E.,
Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P.,
Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A.,
Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A.,
Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T.,
Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D.,
Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X.,
McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C.,
Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S.,
Miller W., Eichler E.E., Bork P., Suyama M., Torrents D.,
Waterston R.H., Wilson R.K.;
"Generation and annotation of the DNA sequences of human chromosomes 2
and 4.";
Nature 434:724-731(2005).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
Venter J.C.;
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 4; 5 AND 6), AND
VARIANT LYS-516.
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[6]
STRUCTURE BY NMR OF 687-738, FUNCTION, PHOSPHORYLATION AT THR-726, AND
INTERACTION WITH PIN1.
PubMed=24267382; DOI=10.1111/febs.12588;
Zucchelli C., Tamburri S., Quilici G., Palagano E., Berardi A.,
Saare M., Peterson P., Bachi A., Musco G.;
"Structure of human Sp140 PHD finger: an atypical fold interacting
with Pin1.";
FEBS J. 281:216-231(2014).
-!- FUNCTION: Component of the nuclear body, also known as nuclear
domain 10, PML oncogenic domain, and KR body (PubMed:8910577). May
be involved in the pathogenesis of acute promyelocytic leukemia
and viral infection (PubMed:8910577). May play a role in
chromatin-mediated regulation of gene expression although it does
not bind to histone H3 tails (PubMed:24267382).
{ECO:0000269|PubMed:24267382, ECO:0000269|PubMed:8910577,
ECO:0000303|PubMed:8910577}.
-!- SUBUNIT: Interacts with PIN1. {ECO:0000269|PubMed:24267382}.
-!- INTERACTION:
Q13526:PIN1; NbExp=4; IntAct=EBI-2865100, EBI-714158;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:8695863,
ECO:0000269|PubMed:8910577}. Nucleus, PML body
{ECO:0000269|PubMed:8695863, ECO:0000269|PubMed:8910577}.
Cytoplasm {ECO:0000269|PubMed:8695863}. Note=Localized to nuclear
structures termed LANDS, for LYSp100-associated nuclear domains.
LANDS are globular, electron-dense structures most often found in
the nucleoplasm, but also found at the nuclear membrane and in the
cytoplasm, suggesting that these structures may traffic between
the cytoplasm and the nucleus (PubMed:8695863). Also colocalizes
with PML in a subset of PML nuclear bodies (PubMed:8910577).
{ECO:0000269|PubMed:8695863, ECO:0000269|PubMed:8910577}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=6;
Name=LYSp100-B {ECO:0000303|PubMed:8695863};
IsoId=Q13342-1; Sequence=Displayed;
Name=LYSp100-A {ECO:0000303|PubMed:8695863};
IsoId=Q13342-2; Sequence=VSP_000560, VSP_000561, VSP_000562;
Name=Sp140 {ECO:0000303|PubMed:8695863};
IsoId=Q13342-3; Sequence=VSP_055922, VSP_000558, VSP_000559;
Name=4;
IsoId=Q13342-4; Sequence=VSP_043235, VSP_043236;
Note=No experimental confirmation available.;
Name=5;
IsoId=Q13342-5; Sequence=VSP_055924;
Note=No experimental confirmation available.;
Name=6;
IsoId=Q13342-6; Sequence=VSP_055923, VSP_000560;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: High levels in spleen and peripheral blood
leukocytes, much lower levels in tonsils, thymus, prostate, ovary,
small intestine, and colon (PubMed:8695863, PubMed:8910577.) Very
low levels in heart, brain, placenta, lung, liver, skeletal
muscle, kidney, and pancreas (PubMed:8910577). Not detected in
brain, liver and muscle (PubMed:8695863).
{ECO:0000269|PubMed:8695863, ECO:0000269|PubMed:8910577}.
-!- INDUCTION: By gamma-interferon. {ECO:0000269|PubMed:8910577}.
-!- PTM: Phosphorylation at Thr-726 promotes binding of PIN1 and
subsequent isomerization of Pro-727.
{ECO:0000269|PubMed:24267382}.
-!- MISCELLANEOUS: This antigen is recognized by autoantibodies from
patients with primary biliary cirrhosis.
{ECO:0000269|PubMed:8910577}.
-!- SEQUENCE CAUTION:
Sequence=AAB18617.1; Type=Frameshift; Positions=862; Evidence={ECO:0000305};
Sequence=AAX93282.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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EMBL; U36499; AAB18616.1; -; mRNA.
EMBL; U36500; AAB18617.1; ALT_FRAME; mRNA.
EMBL; U63420; AAC50817.1; -; mRNA.
EMBL; AC009949; AAX88868.1; -; Genomic_DNA.
EMBL; AC009950; AAX93282.1; ALT_SEQ; Genomic_DNA.
EMBL; CH471063; EAW70922.1; -; Genomic_DNA.
EMBL; BC105743; AAI05744.1; -; mRNA.
EMBL; BC105960; AAI05961.1; -; mRNA.
EMBL; BC070160; AAH70160.1; -; mRNA.
CCDS; CCDS33392.1; -. [Q13342-4]
CCDS; CCDS42831.1; -. [Q13342-1]
CCDS; CCDS63149.1; -. [Q13342-3]
CCDS; CCDS63150.1; -. [Q13342-5]
CCDS; CCDS63151.1; -. [Q13342-6]
PIR; G02099; G02099.
RefSeq; NP_001005176.1; NM_001005176.2. [Q13342-4]
RefSeq; NP_001265380.1; NM_001278451.1. [Q13342-5]
RefSeq; NP_001265381.1; NM_001278452.1. [Q13342-6]
RefSeq; NP_001265382.1; NM_001278453.1. [Q13342-3]
RefSeq; NP_009168.4; NM_007237.4. [Q13342-1]
UniGene; Hs.632549; -.
PDB; 2MD7; NMR; -; B=687-738.
PDB; 2MD8; NMR; -; C=687-738.
PDBsum; 2MD7; -.
PDBsum; 2MD8; -.
ProteinModelPortal; Q13342; -.
SMR; Q13342; -.
BioGrid; 116422; 1.
IntAct; Q13342; 3.
MINT; MINT-6631209; -.
STRING; 9606.ENSP00000375899; -.
ChEMBL; CHEMBL3108643; -.
iPTMnet; Q13342; -.
PhosphoSitePlus; Q13342; -.
BioMuta; SP140; -.
DMDM; 218511671; -.
EPD; Q13342; -.
MaxQB; Q13342; -.
PaxDb; Q13342; -.
PeptideAtlas; Q13342; -.
PRIDE; Q13342; -.
Ensembl; ENST00000343805; ENSP00000342096; ENSG00000079263. [Q13342-6]
Ensembl; ENST00000373645; ENSP00000362749; ENSG00000079263. [Q13342-4]
Ensembl; ENST00000392045; ENSP00000375899; ENSG00000079263. [Q13342-1]
Ensembl; ENST00000417495; ENSP00000393618; ENSG00000079263. [Q13342-3]
Ensembl; ENST00000420434; ENSP00000398210; ENSG00000079263. [Q13342-5]
GeneID; 11262; -.
KEGG; hsa:11262; -.
UCSC; uc002vqj.4; human. [Q13342-1]
CTD; 11262; -.
DisGeNET; 11262; -.
EuPathDB; HostDB:ENSG00000079263.18; -.
GeneCards; SP140; -.
HGNC; HGNC:17133; SP140.
HPA; HPA006162; -.
HPA; HPA067493; -.
MIM; 608602; gene.
neXtProt; NX_Q13342; -.
OpenTargets; ENSG00000079263; -.
PharmGKB; PA38205; -.
eggNOG; KOG2177; Eukaryota.
eggNOG; ENOG4111G04; LUCA.
GeneTree; ENSGT00510000046835; -.
HOGENOM; HOG000089984; -.
HOVERGEN; HBG006294; -.
InParanoid; Q13342; -.
OMA; SSPRCEP; -.
OrthoDB; EOG091G01MN; -.
PhylomeDB; Q13342; -.
TreeFam; TF335091; -.
ChiTaRS; SP140; human.
GenomeRNAi; 11262; -.
PRO; PR:Q13342; -.
Proteomes; UP000005640; Chromosome 2.
Bgee; ENSG00000079263; -.
CleanEx; HS_SP140; -.
ExpressionAtlas; Q13342; baseline and differential.
Genevisible; Q13342; HS.
GO; GO:0001650; C:fibrillar center; IDA:HPA.
GO; GO:0005739; C:mitochondrion; IDA:HPA.
GO; GO:0005635; C:nuclear envelope; TAS:ProtInc.
GO; GO:0005654; C:nucleoplasm; TAS:ProtInc.
GO; GO:0005634; C:nucleus; TAS:ProtInc.
GO; GO:0016605; C:PML body; IEA:UniProtKB-SubCell.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0003700; F:transcription factor activity, sequence-specific DNA binding; TAS:ProtInc.
GO; GO:0006952; P:defense response; TAS:ProtInc.
Gene3D; 1.20.920.10; -; 1.
Gene3D; 3.10.390.10; -; 1.
Gene3D; 3.30.40.10; -; 1.
InterPro; IPR001487; Bromodomain.
InterPro; IPR036427; Bromodomain-like_sf.
InterPro; IPR004865; HSR_dom.
InterPro; IPR000770; SAND_dom.
InterPro; IPR010919; SAND_dom-like.
InterPro; IPR030411; SP140.
InterPro; IPR019786; Zinc_finger_PHD-type_CS.
InterPro; IPR011011; Znf_FYVE_PHD.
InterPro; IPR001965; Znf_PHD.
InterPro; IPR019787; Znf_PHD-finger.
InterPro; IPR013083; Znf_RING/FYVE/PHD.
PANTHER; PTHR13711:SF231; PTHR13711:SF231; 1.
Pfam; PF00439; Bromodomain; 1.
Pfam; PF03172; HSR; 1.
Pfam; PF01342; SAND; 1.
SMART; SM00297; BROMO; 1.
SMART; SM00249; PHD; 1.
SMART; SM00258; SAND; 1.
SUPFAM; SSF47370; SSF47370; 1.
SUPFAM; SSF57903; SSF57903; 1.
SUPFAM; SSF63763; SSF63763; 1.
PROSITE; PS50014; BROMODOMAIN_2; 1.
PROSITE; PS51414; HSR; 1.
PROSITE; PS50864; SAND; 1.
PROSITE; PS01359; ZF_PHD_1; 1.
PROSITE; PS50016; ZF_PHD_2; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Bromodomain; Complete proteome;
Cytoplasm; DNA-binding; Metal-binding; Nucleus; Phosphoprotein;
Polymorphism; Reference proteome; Zinc; Zinc-finger.
CHAIN 1 867 Nuclear body protein SP140.
/FTId=PRO_0000211206.
DOMAIN 22 138 HSR. {ECO:0000255|PROSITE-
ProRule:PRU00747}.
DOMAIN 580 661 SAND. {ECO:0000255|PROSITE-
ProRule:PRU00185}.
DOMAIN 796 829 Bromo. {ECO:0000255|PROSITE-
ProRule:PRU00035}.
ZN_FING 690 736 PHD-type. {ECO:0000255|PROSITE-
ProRule:PRU00146}.
MOTIF 495 514 Nuclear localization signal.
{ECO:0000255}.
COMPBIAS 784 787 Poly-Tyr.
MOD_RES 726 726 Phosphothreonine.
{ECO:0000269|PubMed:24267382}.
VAR_SEQ 136 172 VCYEHSPLQMNNVNDLEDRPRLLPYGKQENSNACHEM ->
ENLSSSAVLCQLVSPNKDWRSHEESLAHTGTLRRSCM (in
isoform 4).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_043235.
VAR_SEQ 173 867 Missing (in isoform 4).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_043236.
VAR_SEQ 219 221 Missing (in isoform Sp140).
{ECO:0000303|PubMed:8910577}.
/FTId=VSP_055922.
VAR_SEQ 222 247 Missing (in isoform 6).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_055923.
VAR_SEQ 248 297 Missing (in isoform Sp140).
{ECO:0000303|PubMed:8910577}.
/FTId=VSP_000558.
VAR_SEQ 326 386 Missing (in isoform Sp140).
{ECO:0000303|PubMed:8910577}.
/FTId=VSP_000559.
VAR_SEQ 353 386 Missing (in isoform LYSp100-A and isoform
6). {ECO:0000303|PubMed:15489334,
ECO:0000303|PubMed:8695863}.
/FTId=VSP_000560.
VAR_SEQ 387 413 Missing (in isoform 5).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_055924.
VAR_SEQ 405 446 SSSLARRGSVSSELENHPMNEEGESEELASSLLYDNVPGAE
Q -> QKQGRKVIKRVAQWILWILQTTPLWENPRGKEEKRG
GMAGAE (in isoform LYSp100-A).
{ECO:0000303|PubMed:8695863}.
/FTId=VSP_000561.
VAR_SEQ 447 867 Missing (in isoform LYSp100-A).
{ECO:0000303|PubMed:8695863}.
/FTId=VSP_000562.
VARIANT 356 356 L -> F (in dbSNP:rs3820975).
/FTId=VAR_055555.
VARIANT 512 512 M -> T (in dbSNP:rs4972945).
/FTId=VAR_055556.
VARIANT 516 516 E -> K (in dbSNP:rs4972946).
{ECO:0000269|PubMed:15489334,
ECO:0000269|PubMed:8910577}.
/FTId=VAR_055557.
VARIANT 558 558 R -> C (in dbSNP:rs11887179).
/FTId=VAR_055558.
CONFLICT 186 186 P -> A (in Ref. 1; AAB18616/AAB18617 and
2; AAC50817). {ECO:0000305}.
CONFLICT 356 358 LSA -> FST (in Ref. 1; AAB18617).
{ECO:0000305}.
CONFLICT 457 457 V -> D (in Ref. 5; AAI05744).
{ECO:0000305}.
CONFLICT 838 838 D -> G (in Ref. 1; AAB18617).
{ECO:0000305}.
CONFLICT 862 862 E -> G (in Ref. 1; AAB18617).
{ECO:0000305}.
HELIX 694 697 {ECO:0000244|PDB:2MD7}.
HELIX 706 712 {ECO:0000244|PDB:2MD7}.
HELIX 715 717 {ECO:0000244|PDB:2MD7}.
STRAND 722 724 {ECO:0000244|PDB:2MD7}.
HELIX 731 735 {ECO:0000244|PDB:2MD7}.
SEQUENCE 867 AA; 98223 MW; 355601D1D4689A74 CRC64;
MAQQGQQGQM ASGDSNLNFR MVAEIQNVEG QNLQEQVCPE PIFRFFRENK VEIASAITRP
FPFLMGLRDR SFISEQMYEH FQEAFRNLVP VTRVMYCVLS ELEKTFGWSH LEALFSRINL
MAYPDLNEIY RSFQNVCYEH SPLQMNNVND LEDRPRLLPY GKQENSNACH EMDDIAVPQE
ALSSSPRCEP GFSSESCEQL ALPKAGGGDA EDAPSLLPGG GVSCKLAIQI DEGESEEMPK
LLPYDTEVLE SNGMIDAART YSTAPGEKQG EEEGRNSPRK RNQDKEKYQE SPEGRDKETF
DLKTPQVTNE GEPEKGLCLL PGEGEEGSDD CSEMCDGEEP QEASSSLARC GSVSCLSAET
FDLKTPQVTN EGEPEKELSL LPGEGEEGSD DCSEMCDGEE RQEASSSLAR RGSVSSELEN
HPMNEEGESE ELASSLLYDN VPGAEQSAYE NEKCSCVMCF SEEVPGSPEA RTESDQACGT
MDTVDIANNS TLGKPKRKRR KKRGHGWSRM RMRRQENSQQ NDNSKADGQV VSSEKKANVN
LKDLSKIRGR KRGKPGTRFT QSDRAAQKRV RSRASRKHKD ETVDFKAPLL PVTCGGVKGI
LHKKKLQQGI LVKCIQTEDG KWFTPTEFEI KGGHARSKNW RLSVRCGGWP LRWLMENGFL
PDPPRIRYRK KKRILKSQNN SSVDPCMRNL DECEVCRDGG ELFCCDTCSR VFHEDCHIPP
VEAERTPWNC IFCRMKESPG SQQCCQESEV LERQMCPEEQ LKCEFLLLKV YCCSESSFFA
KIPYYYYIRE ACQGLKEPMW LDKIKKRLNE HGYPQVEGFV QDMRLIFQNH RASYKYKDFG
QMGFRLEAEF EKNFKEVFAI QETNGNN


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